KMC
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refresh-bio
Fast and frugal disk based k-mer counter
Hello, in my project I would like to just calculate the kmer counts for one side of the reads, read_1.fq.gz, for example. And then afterwards, I would like to compare...
This adds cmake-based build system instead of manually written Makefiles. Included benefits: - Variety of cmake-supported makefile generators (e.g. Ninja or VCPP project files) - More flexibility in options, targets,...
Hello, I used the installation package KMC-3.2.1.tar.gz when installing the KMC software, but after unpacking and running the make installation, I couldn't find the smudge pairs program I wanted to...
For most of the time I've been using kmc it has been working with few issues. However I recently had to start working with .fastq file data stored on a...
I'd like to understand why kmc gives an empty output for several genomes. The genome I downloaded and tried to analyze was [https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/067/135/GCF_001067135.1_ASM106713v1/GCF_001067135.1_ASM106713v1_genomic.fna.gz](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/067/135/GCF_001067135.1_ASM106713v1/GCF_001067135.1_ASM106713v1_genomic.fna.gz) (saved as GCF_001067135.1.fna.gz) The following commands were...
I tried to run kmc (version 3.2.2) on fasta files downloaded from the NCBI ftp server. The program gave only the following error message: Error: unknown exception After many hours...
Hello, first of all, thank you for giving us KMC and kmc_tools, which I use frequently. Now I am trying to retrieve contigs from a genome assembly which contain kmers...
I am doing this: `kmc -k31 -fm @fna_list.txt @kmc_out $PWD` is there a syntax for specifying kmc output database filename as per the list of provided list_of_fasta as input? What...
Hello, I was wondering if it is possible to run stage 1 and stage 2 separately? The reason why I am asking is that I am trying to optimize how...
Kmc runs but gives all zeros for output when run on fastq headers with white space like @alph-63_S41_R1_001:2/1 cD:i:1 cE:f:0.000000 cM:i:0 If I first strip headers to contain no whitespace...
